Why do I get "! You can't use a prefix with `the character 0'." when using \ifnum?

The problem isn't in the \ifnum, but in the use of \global\valueC. The use of \global is intended for use with definitions or assignments, to specify the scope of the definition or assignment. So \global\def... or \global\let... are typical. Since \valueC is not a definition or an assignment, the syntax \global\valueC does not mean anything useful.

I am not sure what was intended by \global\valueC, but if you mean to make the definition of \valueC global, you can use \global\let\valueC\valueC. [I also changed \item to \xitem, because using an already defined command makes me squeamish]

\documentclass{article}
\usepackage{pgffor}
\newcommand\addcolor[1]{%
  \foreach \xitem [count=\step] in {#1} {%
    \ifnum\step=1 \pgfmathsetmacro\valueC{\xitem}\fi%
    \ifnum\step=2 \pgfmathsetmacro\valueM{\xitem}\fi%
    \ifnum\step=3 \pgfmathsetmacro\valueY{\xitem}\fi%
    \ifnum\step=4 \pgfmathsetmacro\valueK{\xitem}\fi%
    \global\let\valueC\valueC\global\let\valueM\valueM%
    \global\let\valueY\valueY\global\let\valueK\valueK%
  }%
}%
\addcolor{0,20,100,0}
\begin{document}
\section{Current CMYK Values}
C:\valueC{} M:\valueM{} Y:\valueY{} K:\valueK
\end{document}

Joseph suggests an even more streamlined approach:

\documentclass{article}
\usepackage{pgffor}
\newcommand\addcolor[1]{%
  \foreach \xitem [count=\step] in {#1} {%
    \pgfmathsetmacro\temp{\xitem}
    \ifnum\step=1 \global\let\valueC\temp\fi%
    \ifnum\step=2 \global\let\valueM\temp\fi%
    \ifnum\step=3 \global\let\valueY\temp\fi%
    \ifnum\step=4 \global\let\valueK\temp\fi%
  }%
}%
\addcolor{0,20,100,0}
\begin{document}
\section{Current CMYK Values}
C:\valueC{} M:\valueM{} Y:\valueY{} K:\valueK
\end{document}

Finally, here is a way with \listofitems:

\documentclass{article}
\usepackage{pgffor,listofitems}
\newcommand\addcolor[1]{%
  \setsepchar{,}%
  \readlist\cvalues{#1}%
  \readlist\clabels{C,M,Y,K}%
  \readlist\cquence{1,2,3,4}%
  \foreachitem\xitem\in\cquence{%
    \pgfmathsetmacro\temp{\cvalues[\xitem]}%
    \expandafter\global\expandafter\let\csname value\clabels[\xitem]\endcsname\temp%
  }%
}%
\addcolor{0,20,100,0}
\begin{document}
\section{Current CMYK Values}
C:\valueC{} M:\valueM{} Y:\valueY{} K:\valueK
\end{document}

You're using a sledgehammer; anyway, \global\valueC is illegal and should be

\global\let\valueC\valueC

But there's a better way:

\documentclass{article}
\usepackage{pgf}

\makeatletter
\newcommand\addcolor[1]{%
  \add@color#1\@nil
}
\def\add@color#1,#2,#3,#4\@nil{%
  \pgfmathsetmacro\valueC{#1}%
  \pgfmathsetmacro\valueM{#2}%
  \pgfmathsetmacro\valueY{#3}%
  \pgfmathsetmacro\valueK{#4}%
}
\makeatother

\begin{document}

\addcolor{0,20,100,0}
C:\valueC \quad M:\valueM \quad Y:\valueY \quad K:\valueK

\addcolor{1,2*3,3+12,4}
C:\valueC \quad M:\valueM \quad Y:\valueY \quad K:\valueK

\end{document}

An even easier way:

\documentclass{article}
\usepackage{xparse}

\ExplSyntaxOn
\NewDocumentCommand\addcolor{m}
 {
  \tl_set:Nx \valueC { \fp_eval:n { \clist_item:nn { #1 } { 1 } } }
  \tl_set:Nx \valueM { \fp_eval:n { \clist_item:nn { #1 } { 2 } } }
  \tl_set:Nx \valueY { \fp_eval:n { \clist_item:nn { #1 } { 3 } } }
  \tl_set:Nx \valueK { \fp_eval:n { \clist_item:nn { #1 } { 4 } } }
}
\ExplSyntaxOff

\begin{document}

\addcolor{0,20,100,0}
C:\valueC \quad M:\valueM \quad Y:\valueY \quad K:\valueK

\addcolor{1,2*3,3+12,4}
C:\valueC \quad M:\valueM \quad Y:\valueY \quad K:\valueK

\end{document}